Water-gas shift reaction on Pt(111).

This tutorial is intended to show how to use pyZacros from a Zacros perspective. Thus, we will literally show how to translate the Zacros input files to a pyZacros script. To do that, we use the system described in the Zacros tutorial Mapping DFT Energies to Zacros Input as an example. All physical/chemical description of the system is described in detail there. This example shows how to include gas species, transition states, as well as stable surface species, and the lateral interactions between them. All information about the energetics is obtained via density functional theory (DFT) calculations. Importantly, lateral interactions are also discussed and included in the example’s script. We invited you first to get familiar with the tutorial cited above to quickly appreciate the parallel between the Zacros input files and the pyZacros objects. This will allow you to follow line-by-line the example’s python script easily.

You can download the example’s python script from this link WaterGasShiftOnPt111.py.

If everything is working well, you should get the following information in the standard output and the figure shown at the end.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
$ amspython WaterGasShiftOnPt111.py
[14.02|16:30:47] PLAMS working folder: /home/user/pyzacros/examples/WaterGasShiftOnPt111/plams_workdir
---------------------------------------------------------------------
simulation_input.dat
---------------------------------------------------------------------
random_seed         123278
temperature          500.0
pressure              10.0

snapshots                 on time       0.0005
process_statistics        on time       0.0005
species_numbers           on time       0.0005
event_report      off
max_steps         infinity
max_time          250.0
wall_time         30

n_gas_species    4
gas_specs_names              CO           H2          H2O          CO2
gas_energies        0.00000e+00  0.00000e+00  0.00000e+00 -6.15000e-01
gas_molec_weights   2.79949e+01  2.01560e+00  1.80105e+01  4.39898e+01
gas_molar_fracs     1.00000e-05  0.00000e+00  9.50000e-01  0.00000e+00

n_surf_species    6
surf_specs_names         CO*        H*      H2O*       OH*        O*     COOH*
surf_specs_dent            1         1         1         1         1         1

finish
---------------------------------------------------------------------
lattice_input.dat
---------------------------------------------------------------------
lattice default_choice
  hexagonal_periodic 1.0 8 10
end_lattice
---------------------------------------------------------------------
energetics_input.dat
---------------------------------------------------------------------
energetics

cluster CO_point
  sites 1
  lattice_state
    1 CO* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng -2.07700e+00
end_cluster

cluster H2O_point
  sites 1
  lattice_state
    1 H2O* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng -3.62000e-01
end_cluster

cluster OH_point
  sites 1
  lattice_state
    1 OH* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng  8.30000e-01
end_cluster

cluster O_point
  sites 1
  lattice_state
    1 O* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng  1.29800e+00
end_cluster

cluster H_point
  sites 1
  lattice_state
    1 H* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng -6.19000e-01
end_cluster

cluster COOH_point
  sites 1
  lattice_state
    1 COOH* 1
  site_types 1
  graph_multiplicity 1
  cluster_eng -1.48700e+00
end_cluster

cluster CO_pair_1NN
  sites 2
  neighboring 1-2
  lattice_state
    1 CO* 1
    2 CO* 1
  site_types 1 1
  graph_multiplicity 1
  cluster_eng  5.60000e-01
end_cluster

cluster OH_H_1NN
  sites 2
  neighboring 1-2
  lattice_state
    1 OH* 1
    2 H* 1
  site_types 1 1
  graph_multiplicity 1
  cluster_eng  2.10000e-02
end_cluster

cluster O_H_1NN
  sites 2
  neighboring 1-2
  lattice_state
    1 O* 1
    2 H* 1
  site_types 1 1
  graph_multiplicity 1
  cluster_eng  1.98000e-01
end_cluster

cluster CO_OH_1NN
  sites 2
  neighboring 1-2
  lattice_state
    1 CO* 1
    2 OH* 1
  site_types 1 1
  graph_multiplicity 1
  cluster_eng  6.60000e-02
end_cluster

cluster CO_O_1NN
  sites 2
  neighboring 1-2
  lattice_state
    1 CO* 1
    2 O* 1
  site_types 1 1
  graph_multiplicity 1
  cluster_eng  4.23000e-01
end_cluster

end_energetics
---------------------------------------------------------------------
mechanism_input.dat
---------------------------------------------------------------------
mechanism

reversible_step CO_adsorption
  gas_reacs_prods CO -1
  sites 1
  initial
    1 * 1
  final
    1 CO* 1
  site_types 1
  pre_expon  2.22600e+07
  pe_ratio  2.13700e-06
  activ_eng  0.00000e+00
end_reversible_step

reversible_step H2_dissoc_adsorp
  gas_reacs_prods H2 -1
  sites 2
  neighboring 1-2
  initial
    1 * 1
    2 * 1
  final
    1 H* 1
    2 H* 1
  site_types 1 1
  pre_expon  8.29900e+07
  pe_ratio  7.96600e-06
  activ_eng  0.00000e+00
end_reversible_step

reversible_step H2O_adsorption
  gas_reacs_prods H2O -1
  sites 1
  initial
    1 * 1
  final
    1 H2O* 1
  site_types 1
  pre_expon  2.77600e+02
  pe_ratio  2.66500e-06
  activ_eng  0.00000e+00
end_reversible_step

reversible_step H2O_dissoc_adsorp
  sites 2
  neighboring 1-2
  initial
    1 H2O* 1
    2 * 1
  final
    1 OH* 1
    2 H* 1
  site_types 1 1
  pre_expon  1.04200e+13
  pe_ratio  1.00000e+00
  activ_eng  7.77000e-01
end_reversible_step

reversible_step OH_decomposition
  sites 2
  neighboring 1-2
  initial
    1 * 1
    2 OH* 1
  final
    1 O* 1
    2 H* 1
  site_types 1 1
  pre_expon  1.04200e+13
  pe_ratio  1.00000e+00
  activ_eng  9.40000e-01
end_reversible_step

reversible_step COOH_formation
  sites 2
  neighboring 1-2
  initial
    1 CO* 1
    2 OH* 1
  final
    1 * 1
    2 COOH* 1
  site_types 1 1
  pre_expon  1.04200e+13
  pe_ratio  1.00000e+00
  activ_eng  4.05000e-01
end_reversible_step

step COOH_decomposition
  gas_reacs_prods CO2 1
  sites 2
  neighboring 1-2
  initial
    1 COOH* 1
    2 * 1
  final
    1 * 1
    2 H* 1
  site_types 1 1
  pre_expon  1.04200e+13
  activ_eng  8.52000e-01
end_step

step CO_oxidation
  gas_reacs_prods CO2 1
  sites 2
  neighboring 1-2
  initial
    1 CO* 1
    2 O* 1
  final
    1 * 1
    2 * 1
  site_types 1 1
  pre_expon  1.04200e+13
  activ_eng  9.88000e-01
end_step

end_mechanism
[14.02|16:30:47] JOB plamsjob STARTED
[14.02|16:30:47] JOB plamsjob RUNNING
[14.02|16:31:17] JOB plamsjob FINISHED
[14.02|16:31:17] JOB plamsjob SUCCESSFUL
[14.02|16:31:27] PLAMS run finished. Goodbye
/scm-uploads/doc.2022/pyzacros/_images/example_WaterGasShiftOnPt111.png